COVID-19 neutrophils preferentially transitioned from the apex of the trajectory, which was an immature state (TOP2A-expressing; Extended Data Fig. 4r) to an IFNactive state characterized by IFITM1, IFITM2 and IFI6 expression (clusters 1–4 and 5; Fig. 1i; Online Atlas) and activation of type I IFN signaling pathways (Extended Data Fig. 3g). Here, IFI6 is linked to COVID-19.